Dear bioconductors£º Yesterday I installed the package ShortRead_1.8.2.tar.gz via the command ," R CMD INSTALL ./pkg2/ShortRead_1.8.2.tar.gz -l ./library/ ".However ,the error happened with the message in the attachment.The error message is below: * installing *source* package 'ShortRead' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 checking for gzeof in -lz... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c alphabet.c -o alphabet.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c io.c -o io.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c io_bowtie.c -o io_bowtie.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c io_soap.c -o io_soap.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c pileup.c -o pileup.o g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -c readBfaToc.cc -o readBfaToc.o g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -c read_maq_map.cc -o read_maq_map.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c sampler.c -o sampler.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c util.c -o util.o gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" -fpic -g -O2 -c xsnap.c -o xsnap.o g++ -shared -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz installing to /ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/ShortRead/libs ** R ** inst ** preparing package for lazy loading Attaching package: 'IRanges' The following object(s) are masked from 'package:base': Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table Error in eval(expr, envir, enclos) : could not find function "setRefClass" Error : unable to load R code in package 'ShortRead' ERROR: lazy loading failed for package 'ShortRead' * removing 'home/xjb/R/bin/lib64/R/library/ShortRead' Can you help me to solve the problem? Thanks. Hope for your reply. BEST! JiaBao Xu [[alternative HTML version deleted]]

On Tue, Jan 18, 2011 at 5:46 PM, xujiabao <xujiabao@genomics.org.cn> wrote: > Dear bioconductors£º > Yesterday I installed the package ShortRead_1.8.2.tar.gz via the > command ," R CMD INSTALL ./pkg2/ShortRead_1.8.2.tar.gz -l ./library/ > ".However ,the error happened with the message in the attachment.The error > message is below: > > > * installing *source* package 'ShortRead' ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking size of unsigned long... 8 > checking for gzeof in -lz... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c alphabet.c -o alphabet.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c io.c -o io.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c io_bowtie.c -o io_bowtie.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c io_soap.c -o io_soap.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c pileup.c -o pileup.o > g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 > -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -c > readBfaToc.cc -o readBfaToc.o > g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" > -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 > -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 > -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 > -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic -g -O2 -c > read_maq_map.cc -o read_maq_map.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c sampler.c -o sampler.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c util.c -o util.o > gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include > -I/usr/local/include > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include" > -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include" > -fpic -g -O2 -c xsnap.c -o xsnap.o > g++ -shared -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o > IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o > pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz > installing to > /ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/ShortRead/libs > ** R > ** inst > ** preparing package for lazy loading > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin, > pmin.int, rbind, rep.int, table > > Error in eval(expr, envir, enclos) : > could not find function "setRefClass" > Error : unable to load R code in package 'ShortRead' > ERROR: lazy loading failed for package 'ShortRead' > * removing 'home/xjb/R/bin/lib64/R/library/ShortRead' > > > Can you help me to solve the problem? Thanks. Hope for your reply. > > Hello JiaBao, The recommended way to install a package is from within R using the biocLite() function. This takes care of installing the appropriate package for your version of R. Try this: source("http://bioconductor.org/biocLite.R") biocLite("ShortRead") If you still have problems, please post the output of those commands, plus the output of sessionInfo(). Thanks, Dan BEST! > > JiaBao Xu > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]